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Magnesium in PDB 6wo9: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg, PDB code: 6wo9 was solved by G.N.Zong, H.C.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.73 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.291, 59.777, 62.463, 90, 90, 90
R / Rfree (%) 18.1 / 22.8

Other elements in 6wo9:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg (pdb code 6wo9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg, PDB code: 6wo9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wo9

Go back to Magnesium Binding Sites List in 6wo9
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:37.3
occ:1.00
 O27 A:O81401 1.9 44.1 1.0
O21 A:O81401 2.0 35.3 1.0
O A:HOH540 2.1 28.0 1.0
O A:GLY50 2.2 16.8 1.0
O36 A:O81401 2.3 47.8 1.0
OE1 A:GLU70 2.3 28.6 1.0
P7 A:O81401 3.2 43.5 1.0
P1 A:O81401 3.2 40.2 1.0
CD A:GLU70 3.3 25.2 1.0
C A:GLY50 3.3 18.7 1.0
MG A:MG403 3.4 57.2 1.0
P6 A:O81401 3.4 51.6 1.0
O41 A:O81401 3.5 40.1 1.0
CA A:GLY51 3.5 19.6 1.0
O16 A:O81401 3.5 53.2 1.0
OE2 A:GLU70 3.7 23.0 1.0
N A:GLY51 3.9 19.4 1.0
O11 A:O81401 4.0 46.2 1.0
O A:HOH554 4.0 56.6 1.0
O37 A:O81401 4.1 35.7 1.0
O46 A:O81401 4.1 48.1 1.0
NH1 A:ARG20 4.2 21.2 1.0
O47 A:O81401 4.2 46.2 1.0
O A:HOH527 4.3 26.6 1.0
OE2 A:GLU66 4.3 33.2 1.0
O31 A:O81401 4.5 30.0 1.0
CA A:GLY50 4.5 18.5 1.0
N A:GLY50 4.6 16.9 1.0
CG A:GLU70 4.6 22.3 1.0
C6 A:O81401 4.6 48.3 1.0
C1 A:O81401 4.7 48.5 1.0
O26 A:O81401 4.7 49.3 1.0
MG A:MG404 4.9 63.5 1.0
C A:GLY51 4.9 18.7 1.0
NH2 A:ARG115 5.0 30.0 1.0

Magnesium binding site 2 out of 3 in 6wo9

Go back to Magnesium Binding Sites List in 6wo9
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:57.2
occ:1.00
 O27 A:O81401 2.1 44.1 1.0
O A:HOH571 2.3 56.6 1.0
O A:HOH554 2.5 56.6 1.0
MG A:MG404 2.5 63.5 1.0
OE2 A:GLU66 2.6 33.2 1.0
OE1 A:GLU70 2.7 28.6 1.0
P7 A:O81401 3.1 43.5 1.0
O A:HOH530 3.3 42.0 1.0
O37 A:O81401 3.4 35.7 1.0
MG A:MG402 3.4 37.3 1.0
O47 A:O81401 3.5 46.2 1.0
CD A:GLU66 3.5 30.0 1.0
CD A:GLU70 3.7 25.2 1.0
OE1 A:GLU66 3.8 38.1 1.0
O36 A:O81401 3.8 47.8 1.0
CG A:GLU70 3.9 22.3 1.0
OE2 A:GLU69 3.9 41.7 1.0
O A:GLY50 4.2 16.8 1.0
CA A:GLY51 4.6 19.6 1.0
O41 A:O81401 4.6 40.1 1.0
OE2 A:GLU70 4.8 23.0 1.0
CG A:GLU66 4.9 27.5 1.0
OD2 A:ASP109 5.0 26.6 1.0
C A:GLY50 5.0 18.7 1.0

Magnesium binding site 3 out of 3 in 6wo9

Go back to Magnesium Binding Sites List in 6wo9
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate (1-IP7) and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:63.5
occ:1.00
 O A:HOH530 1.9 42.0 1.0
O37 A:O81401 2.1 35.7 1.0
OE1 A:GLU66 2.4 38.1 1.0
MG A:MG403 2.5 57.2 1.0
O A:HOH535 2.8 41.9 1.0
P7 A:O81401 3.0 43.5 1.0
O27 A:O81401 3.1 44.1 1.0
CD A:GLU66 3.1 30.0 1.0
OE2 A:GLU66 3.1 33.2 1.0
O47 A:O81401 3.5 46.2 1.0
OE2 A:GLU69 3.9 41.7 1.0
N A:GLY52 4.0 18.3 1.0
O A:HOH571 4.0 56.6 1.0
NH1 A:ARG65 4.2 32.3 1.0
O A:HOH538 4.2 52.6 1.0
CA A:GLY51 4.3 19.6 1.0
O41 A:O81401 4.4 40.1 1.0
O A:HOH554 4.4 56.6 1.0
O A:GLY52 4.6 20.7 1.0
CG A:GLU66 4.6 27.5 1.0
C A:GLY51 4.6 18.7 1.0
CA A:GLY52 4.9 18.6 1.0
MG A:MG402 4.9 37.3 1.0
OE1 A:GLU70 4.9 28.6 1.0

Reference:

G.Zong, N.Jork, S.Hostachy, D.Fiedler, H.J.Jessen, S.B.Shears, H.Wang. New Structural Insights Reveal An Expanded Reaction Cycle For Inositol Pyrophosphate Hydrolysis By Human DIPP1. Faseb J. V. 35 21275 2021.
ISSN: ESSN 1530-6860
PubMed: 33475202
DOI: 10.1096/FJ.202001489R
Page generated: Wed Aug 13 19:50:11 2025

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